Sentinel Site Selection Proposal for Genomic Surveillance in Ethiopia (2020-2024)
Introduction
- Objective: Propose sentinel sites for genomic surveillance in Ethiopia to enhance outbreak detection and response.
- Data Source: Disease surveillance data (2020-2024) covering 4,852 records from total reporting woredas in the above years.
- Diseases:
- Malaria (
mal), Meningitis (mng), AFP Polio (afp), Anthrax (anth), Rabies (rab), Measles (msls): 2020-2024. - Cholera (
chlr): 2022-2024. - Dengue Fever (
deng_fevr): 2023-2024.
- Malaria (
- Goals:
- Identify high-burden woredas for each disease.
- Select woredas with multiple diseases for comprehensive surveillance.
- Visualize results interactively for stakeholder use.
Methodology: Data Collection and Preparation
- Scope: Aggregated disease cases by woreda and region from 2020 to 2024.
- Data Limitations:
- Cholera data available only from 2022-2024.
- Dengue fever data available only from 2023-2024.
- Missing values (
NA) treated as zero to ensure consistent analysis.
- Processing:
- Summed cases per disease per woreda, respecting data availability periods.
- Used
tidyversefor data cleaning and aggregation.
Methodology: Site Selection Process
- Step 1: Ranking Woredas per Disease:
- For each disease, ranked woredas by case count within each region.
- Selected top 20 woredas for Oromia and Amhara (high-population regions).
- Selected top 10 woredas for other regions.
- Step 2: Identifying Multi-Disease Woredas:
- Identified woredas appearing in multiple disease rankings.
- Calculated:
num_diseases: Number of diseases ranked in top 10/20.diseases_present: List of diseases.total_cases: Sum of cases across all diseases (for context).
- Filtered for woredas with at least two diseases.
- Sorted by region,
num_diseases(descending), andtotal_cases(descending).
Methodology: Visualization
- Tools: Used
tmapfor interactive mapping andDTfor tables(Table isnot working now but will be corrected) - Map Components:
- Woredas colored by
num_diseases(Blues palette). - Admin 1 (region) boundaries with labels to show geographic context.
- Popups with details: region, zone, woreda, number of diseases, diseases present, total cases.
- Woredas colored by
- Table:Interactive display of proposed woredas with filtering and sorting capabilities.
- Shapefiles:
- Admin 3 (woredas):
eth_admbnda_adm3_csa_bofedb_2021.shp. - Admin 1 (regions):
eth_admbnda_adm1_csa_bofedb_2021.shp.
- Admin 3 (woredas):
Results: Proposed Sentinel Sites - Interactive Table
- Description:
- Shows woredas with multiple diseases, proposed as sentinel sites.
- Columns:
region,zone,woreda,num_diseases,diseases_present,total_cases.
- How to Access and Use:
- Filter: Use the search bar to find specific regions or woredas.
- Sort: Click column headers (e.g.,
num_diseases) to rank by disease count. - Navigate: Use pagination to view all entries.
- Helps stakeholders identify priority woredas for surveillance.
Results: Proposed Sentinel Sites - Interactive Table
Description:
- Visualizes proposed sentinel sites (woredas with >=2 diseases).
- Colored by number of diseasese ( darker blue = more disease reported)
- Includes Admin 1 boundaries and region names for context.
How to use the map:
- Zoom/Pan: Explore specific regions or woredas.
- Click:View popups with details (region, zone, woreda, diseases, cases).
- Legend: Interpret disease count via the color scale.
- Ideal for spatial analysis and Site prioritization.
Discussion
- Key Findings:
- [Placeholder: e.g., “Oromia and Amhara have multiple woredas with 3+ diseases, ideal for surveillance hubs.”]
- Limited cholera and dengue data may underrepresent some woredas’ burden.
- Implications:
- Multi-disease woredas ensure broad pathogen coverage.
- Limitations:
- Cholera (2022-2024) and dengue (2023-2024) data gaps.
- Potential under reporting or missing data (
NAvalues). - utilization of cases definitions in healht facilites - hence reported cases might not really be cases.
Conclusion
- Summary:
- Proposed sentinel sites based on high disease burden and diversity.
- Interactive table and map generated to facilitate data-driven decisions.
- Next Steps:
- Refine the proposed sites by improving selection approach.
- Validate sites through discussion with regions and field assessments.
- Contact: Henok T ([henoktadesse95@gmail.coml])